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- PDB-1aqg: NMR STRUCTURE OF THE RHODOPSIN-BOUND C-TERMINAL PEPTIDE OF THE TR... -

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Basic information

Entry
Database: PDB / ID: 1aqg
TitleNMR STRUCTURE OF THE RHODOPSIN-BOUND C-TERMINAL PEPTIDE OF THE TRANSDUCIN ALPHA-SUBUNIT, 20 STRUCTURES
ComponentsTRANSDUCIN ALPHA-1 SUBUNIT
KeywordsTRANSDUCER / TRANSDUCIN / RHODOPSIN / GTP-BINDING
Function / homology
Function and homology information


negative regulation of cyclic-nucleotide phosphodiesterase activity / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / acyl binding / photoreceptor outer segment membrane / G alpha (i) signalling events / response to light stimulus / phototransduction / visual perception ...negative regulation of cyclic-nucleotide phosphodiesterase activity / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / acyl binding / photoreceptor outer segment membrane / G alpha (i) signalling events / response to light stimulus / phototransduction / visual perception / photoreceptor inner segment / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / photoreceptor disc membrane / GDP binding / heterotrimeric G-protein complex / GTPase activity / GTP binding / protein kinase binding / metal ion binding
Similarity search - Function
G-protein alpha subunit, group I / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(t) subunit alpha-1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / DISTANCE GEOMETRY, CONSTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING
AuthorsKisselev, O.G. / Marshall, G.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Light-activated rhodopsin induces structural binding motif in G protein alpha subunit.
Authors: Kisselev, O.G. / Kao, J. / Ponder, J.W. / Fann, Y.C. / Gautam, N. / Marshall, G.R.
History
DepositionJul 29, 1997Processing site: BNL
Revision 1.0Jul 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_ensemble / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.solvent_system / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSDUCIN ALPHA-1 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)1,2821
Polymers1,2821
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
Representative

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Components

#1: Protein/peptide TRANSDUCIN ALPHA-1 SUBUNIT / GT(ALPHA)(340-350)


Mass: 1281.521 Da / Num. of mol.: 1 / Fragment: RHODOPSIN BINDING DOMAIN, RESIDUES 340-350 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cell: PHOTORECEPTOR ROD CELL / Cellular location: ROD OUTER SEGMENT DISKS / Organ: EYE / Organelle: ROD OUTER SEGMENTRod cell / Tissue: RETINA / References: UniProt: P04695

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: TRNOESY

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Sample preparation

DetailsType: solution
Contents: 20 mM sodium phosphate, 100 mM KCl, 0.1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O
Label: sample_1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphatenatural abundance1
100 mMKClnatural abundance1
0.1 mMEDTAnatural abundance1
1 mMDTTnatural abundance1
Sample conditionsIonic strength: 120 / pH: 7.5 / Pressure: AMBIENT / Temperature: 274 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

Software
NameClassification
VNMRmodel building
VNMRphasing
NMR software
NameDeveloperClassification
TinkerPONDERrefinement
TinkerPONDERstructure calculation
SYBYLTriposstructure calculation
MOLMOLKoradi, Billeter and Wuthrichstructure calculation
RefinementMethod: DISTANCE GEOMETRY, CONSTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING
Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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